Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function

Figure 3

Dendrogram of AraC/XylS family members annotated with functional categories. A dendrogram of 62 AraC/XylS family members and four proteins found by structural similarity search and whose biological role is unknown or poorly characterized is presented (marked with an asterisk). The tree was constructed using the maximum likelihood optimization criteria and a bootstrap test was conducted with 100 replicates. Bootstrap values greater than 50 are shown as number in the corresponding nodes of the tree. Leaves contain the UniProt or PDB accession code and the protein name. Two classification levels are included in this dendrogram. The inner color strip represents a primary classification (functional category) that contains four general classes as in Figure 2. The outer circle contains several colored shapes that represent a secondary and more specific classification scheme, which provides more detail to the biological process associated with each protein. One or two functional categories were assigned.